Month: February 2016

Will Gervais just posted a really, really cool simulation showing differences in the number of findings discovered by Dr. Power (who runs 100 person per condition studies, all day everyday) and Dr. Wide Net (who runs 25 person per condition pilot studies and follows up on promising – aka statistically significant – ideas). Both researchers have access to a limited number (4,000) of participants in a given year. The question is, which strategy is better for netting creative new ideas?

Luckily for me, Will shared his code. The code is amazing, and Will is modest. It was easy to modify and add a few pieces to find out a few things I wanted to know. Specifically, Will presents the rate of “findings” (aka true positives) that each approach yields. But what about false positives? Missed effects (aka false negatives)? Correct rejections? Are there any differences for these other findings for Dr. Power vs. Dr. Wide Net? My results are below – as figures instead of tables, sorry Will!

Dr. Power is on the right, and Dr. Wide Net is on the left. I ran the simulation at 3 different prior levels (.25, .50, .75), because I’m even lazier than Will claims to be (he’s obviously not, given this awesome sim). The green line represents the total number of ideas tested (I replicate Will’s finding that for Dr. Wide Net, the number of ideas tested goes down as the prior goes up, whereas for Dr. Power, the number of ideas tested is a direct function of n/cell and total N).

The yellow-y line is the number of true positives (“findings”) identified. Just as Will found, I find that as the prior goes up, Dr. Power finds more findings. (Note that my simulation is done with the alpha for Dr. Wide Net’s pilot studies set at .10, so the same as Will’s Table 2).

The purple line is the number of findings that represent true negatives (i.e., no effect exists, and the test returns non-significant). These go down as the prior goes up, definitionally.

The blue line represents the number of misses – true effects that go undetected. Dr. Wide Net has a ton of these! Dr. Power barely misses out on any effects. This makes sense, because Dr. Wide Net is sacrificing power for the ability to test many ideas. Lower power means that there will be more missed true effects, by definition. (However, for both Drs., misses increase as the prior increases. I don’t actually know why this is. Why should power decrease as the prior increases? Readers?)

Now here’s where it gets really strange. It’s almost imperceptible in the graph above, but the rate of false positives is higher for Dr. Power than it is for Dr. Wide Net. Neither doctor has a particularly high false positive rate, but Dr. Power’s rate is higher. What’s going on? My hunch is that Dr. Wide Net’s filtering of the effects she studies (via pilot testing) is helping to lower the overall false positive rate of her studies.

Let’s look at these results another way:

Here we can clearly see that the rate of false positive studies is more perceptible for Dr. Power than Dr. Wide Net (this figure shows the percentage of studies done that yield a particular result). As we know, Dr. Wide Net does way, way more studies.

Another way to think about this is as the False Discovery Rate, or the proportion of statistically significant findings that are false positives. We can also consider the False Omission Rate, the proportion of non-significant findings that are missed (false negatives). Here’s a graph:

Dr. Power does have a higher false discovery rate (but the FDR decreases as the prior increases). Dr. Wide Net’s false discovery rate is almost zero. So this is a little weird, because it almost seems like a win for Dr. Wide Net.

BUT – and there’s always a but!

Dr. Wide Net’s False Omission Rate is off the charts. With a 50-50 prior, about 40% of Dr. Wide Net’s non-significant results are actually real effects. By contrast, with the same prior, Dr. Power has only about 18% non-significant results that are actually real effects. When we take this finding into account together with efficiency (again, Dr. Wide Net has to do tons more studies than Dr. Power), I’m pretty sure the lower false discovery rate isn’t worth it.

My code (a slightly modified version of Will’s) is here. I welcome corrections and comments!

SPSP 2016 has just wrapped up and with it another year of fantastic meetings and discussion. This year, I (together with Jordan Axt, Erica Baranski, and David Condon) hosted a professional development session on daily open science practices – little things you can do each day to make your work more open and reproducible. You can find all of our materials for the session here, but I wanted to elaborate on my portion of the session concerning pre-registration.

A person approached me after the session and told me the following:

“I want to give this pre-registration thing a try, but I don’t know where to start. How can I show an editor that my work is pre-registered?”

So here it is: a how-to guide to pre-registration. As I said at SPSP, there is not one perfect/only way to pre-register – scientists can choose to pre-register only locally (nothing online – just some documentation for themselves), privately (pre-registration plan posted online, but with closed access), or publicly (pre-registration plan posted online, in a registry, and free for all to see). The key ingredient across all of these approaches is that flexibility in analysis and design is constrained by pre-specifying the researcher’s plan (more on that in a bit). For now, let’s consider the options one-by-one.

Pros: Pre-registration in any form helps you slow down and be more sure that your project can test the question you want it to. I would argue that the quality of science improves as a result. You have protection, even if only to yourself and your team, against over-interpreting an exploratory finding (by decreasing hindsight bias or reducing hypothesizing after the results are known, aka HARKing).

Cons: An editor or reviewer doesn’t have evidence, apart from your word, that the pre-registration actually happened. A scientist’s word is worth a lot, but when it comes to convincing a skeptic, you might have a tough time.

Options: Your imagination is the limit when it comes to thinking of ways to do internal documentation. You could go old-school and write long-hand in ink in a lab notebook. You could use Evernote or Google docs or some other kind of cloud based document storage. The key is that you make your notes to yourself (and perhaps your local team), and those notes don’t get edited later on. They are just a record of your plans. I should note that you would benefit from using a standard type of template (more on templates in a minute), if only so that you don’t forget to think through the most important factors in your study (trust me, forgetting happens to the best of us).

2. Private pre-registration: Same as internal only pre-registration, except you post the pre-registration privately to a repository. Private pre-registrations can be selectively shared with editors and reviewers, for the purposes of proving that a pre-registration occurred as specified.

Pros: You cannot be “scooped” – meaning your ideas stay private until such time as you later choose, but you can definitively prove that your (perhaps un-Orthodox) analysis was the plan all along.

Cons: You cannot attract collaborators, either. Others working in a similar area don’t know what you’re up to, and you might miss out on a valuable collaboration. For the field writ large, this isn’t a very attractive long term option, because we don’t get a record of abandoned projects either – studies that for whatever reason don’t make it past the data collection stage and into the published literature.

Options: For easy to do private pre-registration, you can’t beat aspredicted.org. One author on the team simply answers 9 questions about the planned project, and a .pdf of the pre-registration is generated. Pre-registrations can stay private indefinitely on aspredicted, but authors do have the option to generate a web link to share with editors/reviewers. Another option would be to use the Open Science Framework (osf.io). The OSF has a pre-registration function that researchers can choose to make private for up to 4 years (at which point, the pre-registration does become public). The pre-registration function freezes the content of an OSF project so that a record of the project is preserved and no longer able to be edited. As an alternative to the pre-registration function, OSF timestamps all researcher activity on the site, and it allows researchers to keep their (non-registered) projects private indefinitely. This means that a researcher could post a document containing a pre-registration to their private project and use the OSF timestamping system to prove to an outside party when the pre-registration occurred, relative to when data were collected. The clunkiness of this system means that researchers who want to have indefinitely private pre-registrations will likely want to use aspredicted.org, or use OSF and accept that after the researcher-determined embargo period of up to 4 years, their pre-registrations will become public. Again, the public vs. private distinction has downstream consequences for the field, because public pre-registrations allow researchers to understand the magnitude of the file drawer problem in a given area of the literature.

3. Public pre-registration: Same as private pre-registration, except that researchers post their plans publicly on the web.

Pros: Fully open, complete with mega-credibility points. Your work is fully verifiable to an outside party. Outside parties can contact you and ask to collaborate. As a side note, we all have projects that are interesting and potentially fruitful, but that get left by the wayside due to lack of time or other constraints. To me, pre-registration (or really any form of transparent documentation) is a way of keeping track of these projects and letting others pick them up as the years go on (I have this fantasy that when a student joins my lab, I’ll be able to direct them to the documentation of an in-progress, but stalled, project, and they’ll just pick it right back up where the previous student faltered). So there are potential benefits of increased transparency and better record keeping beyond the type-I error control that proponents of pre-registration are so quick to note.

Cons: Scooping? I’m not sure this is a real concern, but insofar as people have anxiety about it, it needs to be addressed. If you make your whole train of logic/program of research fully transparent, there is always the risk that someone better/smarter/faster/stronger than you will swoop in and run off with the idea. To me, the potential for fruitful collaborations far outweighs the risk of scooping, and actually both are trumped by a third possibility, which is that all this documentation won’t attract much attention at all. In my own experience, a handful of people are interested, but mostly my work goes on as usual. Others have noted that public pre-registration actually could help you stake a claim on a project, insofar as you are able to demonstrate the temporal precedence of the idea relative to the alleged scoop-er. A final con is that there is a time cost to getting the study materials up to snuff for public consumption. However, as I noted before, the quality of the work likely increases, and the project is less likely to get shelved if a collaborator loses interest or there are other hiccups down the road. I’m a big fan of designing studies so that they are informative, null results or not, so that there is (ideally) no such thing as a “failed” study, and instead only limitations in our time, motivation, and fiscal resources to publish every (properly executed) study. Doing a good job of documentation on the front end of a project means that even if you never get around to publishing a boring/null/whatever result, a future meta-analyst could, with some ease, find your project and incorporate it into their work.

Options: The OSF is likely to be your best bet at this point, and although OSF is a powerful, flexible system, it is not the most user friendly for beginners. However, the opportunity cost of learning the system more than pays for itself down the road. Anna van’t Veer and Roger Giner-Sorolla have this nice step-by-step that explains how to create and pre-register a new project on OSF. The Center for Open Science pre-registration challenge also has a bunch of materials that will help you get started. And if you want to do the pre-registration challenge, and you’re an R user, you’ll definitely want to check out Frederick Aust’s prereg package for R.

Regardless of which option you choose to pursue, I would encourage you to think about using a template (either make your own or use someone else’s) so that you get all of the most important details of your project ironed out ahead of time. It will definitely happen that once you have your data in hand, you realize that you’ve forgotten to specify something important. That’s OK, and you ought to just honestly report such discrepancies and move on. Don’t let perfect be the enemy of done.